[Bioc-sig-seq] Creating A TranscriptDb

[Dario Strbenac]

Please disregard. There were some inconsistent rows in the data.

---- Original message ----
>Date: Mon, 23 May 2011 11:00:01 +1000 (EST)
>From: bioc-sig-sequencing-bounces at r-project.org (on behalf of Dario Strbenac <D.Strbenac at garvan.org.au>)
>Subject: [Bioc-sig-seq] Creating A TranscriptDb  
>To: bioc-sig-sequencing at r-project.org
>
>Hello,
>
>I've read the help page, and I believe my three data frames meet all the requirements, but the creation of the TranscriptDb results in an error message.
>
>My code example is :
>library(GenomicFeatures)
>download.file("http://129.94.136.7/file_dump/dario/dataFramesForTrDB.Rdata", "./3DF.Rdata") # 2.2 MB
>load("3DF.Rdata") # transcripts, splicings, genes.
>db <- makeTranscriptDb(transcripts, splicings, genes)
>
>Error in sqliteExecStatement(con, statement, bind.data) : 
>  RS-DBI driver: (RS_SQLite_exec: could not execute: constraint failed)
>
>Session info is :
>
>R version 2.13.0 (2011-04-13)
>Platform: x86_64-unknown-linux-gnu (64-bit)
>  ...                       ...
>other attached packages:
>[1] GenomicFeatures_1.4.1 GenomicRanges_1.4.5   IRanges_1.10.4       
>
>loaded via a namespace (and not attached):
>[1] Biobase_2.11.10     biomaRt_2.7.2       Biostrings_2.19.18 
>[4] BSgenome_1.19.6     DBI_0.2-5           RCurl_1.6-1        
>[7] RSQLite_0.9-4       rtracklayer_1.11.12 XML_3.4-0 
>
>--------------------------------------
>Dario Strbenac
>Research Assistant
>Cancer Epigenetics
>Garvan Institute of Medical Research
>Darlinghurst NSW 2010
>Australia
>
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>Bioc-sig-sequencing at r-project.org
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--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia